2ICW: PDB entry 2ICW

Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule. Determined by X-ray diffraction at 2.41 Å resolution. Released 20 Mar 2007.

Method: X-ray diffraction
Resolution: 2.41 Å
Organisms: Homo sapiens, Mycoplasma arthritidis, Mus musculus
Chains: 12
Atoms: 13,464
Mol. weight: 188.4 kDa
Released: 20 Mar 2007

Explore 2ICW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ICW contains 55 α-helices and 120 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and D: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-34	6	1
β-strand	41-43	3	1
α-helix	48-51	4
β-strand	53	1	2
α-helix	57-76	20
α-helix	81-84	4
β-strand	85	1	3
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-128	3	5
β-strand	133-134	2	4
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chains B and E: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	6
α-helix	96-97	2
β-strand	98-99	2	7
β-strand	102-103	2	8
β-strand	114-116	3	8
β-strand	119-122	4	7
β-strand	123	1	6
β-strand	128-133	6	9
β-strand	136-137	2	9
β-strand	142-144	3	8
β-strand	148-149	2	7
β-strand	155-157	3	7
β-strand	159-162	4	8
β-strand	170-176	7	9
α-helix	183	1
β-strand	184-189	6	9

Chains C and F: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	307	1	2
α-helix	311-313	3
α-helix	315-317	3

Chain G: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	24-25	2
α-helix	26-33	8
α-helix	39-66	28
α-helix	72-92	21
α-helix	97-122	26
α-helix	126-144	19
α-helix	158-167	10
α-helix	171-175	5
α-helix	177-194	18
α-helix	198-202	5
α-helix	205-210	6

Chain H: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	8-10	3
α-helix	24-25	2
α-helix	26-33	8
α-helix	39-66	28
α-helix	72-92	21
α-helix	97-122	26
α-helix	126-144	19
α-helix	158-167	10
α-helix	171-175	5
α-helix	177-194	18
α-helix	198-202	5
α-helix	205-210	6

Chains I and K: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	19
β-strand	9-12	4	20
β-strand	18-20	3	19
β-strand	23	1	19
β-strand	32-37	6	20
β-strand	44-49	6	20
β-strand	55-57	3	19
β-strand	62-67	6	19
β-strand	72-77	6	19
α-helix	82-84	3
β-strand	87-93	7	20
β-strand	99-101	3	20
β-strand	105-109	5	20

Chains J and L: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-13	4	22
β-strand	19-21	3	23
β-strand	22-25	4	21
β-strand	31-37	7	22
β-strand	44-49	6	22
β-strand	56-57	2	22
β-strand	65-67	3	23
β-strand	73	1	21
β-strand	75-78	4	23
α-helix	83-85	3
β-strand	87-94	8	22
β-strand	99-101	3	22
β-strand	105-109	5	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, D	protein	179	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1-1 beta chain	B, E	protein	190	Homo sapiens	P01911 (AlphaFold model)
haemagglutinin peptide	C, F	protein	13
Mycoplasma arthritidis mitogen	G, H	protein	213	Mycoplasma arthritidis	Q48898 (AlphaFold model)
T-cell receptor alpha chain V	I, K	protein	110	Mus musculus	P01738 (AlphaFold model)
T-cell receptor beta chain V	J, L	protein	113	Mus musculus	A2NTY6

Sequence of entity 1 (A, D), FASTA

>2ICW_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, D)
EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALAN
IAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWL
RNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD

Sequence of entity 2 (B, E), FASTA

>2ICW_2 HLA class II histocompatibility antigen, DRB1-1 beta chain (chains B, E)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRA

Sequence of entity 3 (C, F), FASTA

>2ICW_3 haemagglutinin peptide (chains C, F)
PKYVKQNTLKLAT

Sequence of entity 4 (G, H), FASTA

>2ICW_4 Mycoplasma arthritidis mitogen (chains G, H)
MKLRVENPKKAQKHFVQNLNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHAF
GIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADNDLSY
FISQNKNFQELWDKAVKLTKEMKIKLKGQKLDLRDGEVAINKVRELFGSDKNVKELWWFR
SLLVKGVYLIKRYYEGDIELKTTSDFAKAVFED

Sequence of entity 5 (I, K), FASTA

>2ICW_5 T-cell receptor alpha chain V (chains I, K)
QSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGPQLLLKYYSGDPVVQGVN
GFEAEFSKSNSSFHLRKASVHRSDSAVYFCAVSGFASALTFGSGTKVIVL

Sequence of entity 6 (J, L), FASTA

>2ICW_6 T-cell receptor beta chain V (chains J, L)
EAAVTQSPRNKVAVTGEKVTLSCNQTNNHNNMYWYRQDTGHELRLIHYSYGAGSTEKGDI
PDGYKASRPSQENFSLILESATPSQTSVYFCASGGGGTLYFGAGTRLSVLSSA

Primary citation

Crystal structure of a complete ternary complex of TCR, superantigen and peptide-MHC. Wang, L., Zhao, Y., Li, Z. et al. Nat Struct Mol Biol (2007) 14:169-171. DOI 10.1038/nsmb1193 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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